A specialized database (DB) for Arabidopsis membrane proteins, ARAMEMNON, was designed that facilitates the interpretation of gene and protein sequence data by integrating features that are presently only available from individual sources. Using several publicly available prediction programs, putative integral membrane proteins were identified among the approximately 25,500 proteins in the Arabidopsis genome DBs. By averaging the predictions from seven programs, approximately 6,500 proteins were classified as transmembrane (TM) candidate proteins. Some 1,800 of these contain at least four TM spans and are possibly linked to transport functions. The ARAMEMNON DB enables direct comparison of the predictions of seven different TM span computation programs and the predictions of subcellular localization by eight signal peptide recognition programs. A special function displays the proteins related to the query and dynamically generates a protein family structure. As a first set of proteins from other organisms, all of the approximately 700 putative membrane proteins were extracted from the genome of the cyanobacterium Synechocystis sp. and incorporated in the ARAMEMNON DB. The ARAMEMNON DB is accessible at the URL http://aramemnon.botanik.uni-koeln.de.Biological membranes constitute a chemical barrier to the environment and are thus the prerequisite for the establishment and maintenance of a controlled intracellular milieu, the cytoplasm. In eukaryotes, membranes are also responsible for the formation of chemically distinct intracellular compartments. The lipid bilayer membranes contain a great diversity of proteins that fulfill different functions and serve as an interface to the environment and between different compartments. Among these membrane proteins are receptors involved in signaling cascades and pathogen defense reactions, enzymes such as the apparatus for cell wall biosynthesis, and transporters responsible for the import and export of solutes and ions and the establishment of electrochemical gradients across membranes, thereby connecting the different metabolic pathways of the cellular compartments and organelles.Many plant transport proteins were identified by complementation of yeast mutants that were deficient in certain transport or metabolic functions (Frommer and Ninnemann, 1995). Membrane proteins have a modular structure, consisting of hydrophobic domains and hydrophilic loops or termini that extend into the cytoplasm, the organelle, or point to the extracellular space. The hydrophobic transmembrane (TM) domains consist of amphipathic ␣-helices or -barrels that pass across or dip into the hydrophobic membrane lipid bilayer. During recent years, the three-dimensional structures of more than 160 TM proteins or domains were determined at varying resolution, and it appears that modularity is a general feature of polytopic membrane proteins (http://www.rcsb.org/pdb/; http://www.ncbi.nlm. nih.gov:80/Structure/; Berman et al., 2002;.Arabidopsis is the first plant for which the genome has been deciphered...
SummaryThe Arabidopsis thaliana tpt-1 mutant which is defective in the chloroplast triose phosphate/phosphate translocator (TPT) was isolated by reverse genetics. It contains a T-DNA insertion 24 bp upstream of the start ATG of the TPT gene. The mutant lacks TPT transcripts and triose phosphate (TP)-specific transport activities are reduced to below 5% of the wild type. Analyses of diurnal variations in the contents of starch, soluble sugars and phosphorylated intermediates combined with 14 CO 2 labelling studies showed, that the lack of TP export for cytosolic sucrose biosynthesis was almost fully compensated by both continuous accelerated starch turnover and export of neutral sugars from the stroma throughout the day. The utilisation of glucose 6-phosphate (generated from exported glucose) rather than TP for sucrose biosynthesis in the light bypasses the key regulatory step catalysed by cytosolic fructose 1,6-bisphosphatase. Despite its regulatory role in the feed-forward control of sucrose biosynthesis, variations in the fructose 2,6-bisphosphate content upon illumination were similar in the mutant and the wild type. Crosses of tpt-1 with mutants unable to mobilise starch (sex1) or to synthesise starch (adg1-1) revealed that growth and photosynthesis of the double mutants was severely impaired only when starch biosynthesis, but not its mobilisation, was affected. For tpt-1/sex1 combining a lack in the TPT with a deficiency in starch mobilisation, an additional compensatory mechanism emerged, i.e. the formation and (most likely) fast turnover of high molecular weight polysaccharides. Steady-state RNA levels and transport activities of other phosphate translocators capable of transporting TP remained unaffected in the mutants.
Complementation of a yeast acr1 mutant carrying a deletion of the succinate/fumarate carrier gene enabled functional identification of a mitochondrial succinate translocator from Arabidopsis thaliana (AtmSFC1). Thus complementation of yeast mutants is applicable also for identification and characterization of organellar transporters. Reverse transcription polymerase chain reaction and promoter-GUS fusion showed expression of AtmSFC1 in 2 day old dark grown seedlings, which declined in cotyledons during further development, consistent with a role in export of fumarate for gluconeogenesis during lipid mobilization at early germination of Arabidopsis seeds. In mature plants, expression was found in developing and germinating pollen, suggesting a role in ethanolic fermentation.
BackgroundArginine and citrulline serve as nitrogen storage forms, but are also involved in biosynthetic and catabolic pathways. Metabolism of arginine, citrulline and ornithine is distributed between mitochondria and cytosol. For the shuttle of intermediates between cytosol and mitochondria transporters present on the inner mitochondrial membrane are required. Yeast contains a mitochondrial translocator for ornithine and arginine, Ort1p/Arg11p. Ort1p/Arg11p is a member of the mitochondrial carrier family (MCF) essential for ornithine export from mitochondria. The yeast arg11 mutant, which is deficient in Ort1p/Arg11p grows poorly on media lacking arginine.ResultsHigh-level expression of a nuclear encoded Arabidopsis thaliana homolog (AtmBAC2) of Ort1p/Arg11p was able to suppress the growth deficiency of arg11. RT-PCR analysis demonstrated expression of AtmBAC2 in all tissues with highest levels in flowers. Promoter-GUS fusions showed preferential expression in flowers, i.e. pollen, in the vasculature of siliques and in aborted seeds. Variable expression was observed in leaf vasculature. Induction of the promoter was not observed during the first two weeks in seedlings grown on media containing NH4NO3, arginine or ornithine as sole nitrogen sources.ConclusionAtmBAC2 was isolated as a mitochondrial transporter for arginine in Arabidopsis. The absence of expression in developing seeds and in cotyledons of seedlings indicates that other transporters are responsible for storage and mobilization of arginine in seeds.
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